ABSTRACT Determining new causes for rare and common disease would have major and immediate benefits for patients and their families by improved genetic testing, genetic counseling, insurance reimbursement, and ultimately more effective treatment options. Our long term goal is to disruptively improve and expand genetic testing for rare and common disease. Current diagnostic tests only consider pathogenic variants in protein-coding genes. However, we now have evidence that a substantial fraction of rare disease is due to unknown non-coding genetic variants that influence the regulation of those genes. The goal of this proposal is to identify and quantify the effect of pathogenic non-coding genetic variants on the function and expression of genes that cause rare disease. This initial step will enable treatment early in life when it is still possible to stop the most severe consequences of disease, including death. We will focus on severe early-onset pediatric disorders, including glycogen storage diseases (GSD I, II, III, IV, and IX), and the fatty acid oxidation disorders, very long-chain acyl-CoA dehydrogenase deficiency (VLCAD), and multiple acyl-CoA dehydrogenase deficiency (MADD). To date, genetic tests for these and other diseases are limited to protein-coding mutations. However, our clinical team has collected numerous cases that have a single pathogenic coding variant on only one of the two alleles that must be both affected in these recessive disorders. We also have biochemical and biomarker evidence that supports the diagnosis. Those cases are an ideal opportunity to identify additional disease-causing variants. Our hypothesis is that the genetic causes of recessive disorders include novel genetic variants that can alter either protein sequence (Aim 1), splicing (Aim 2), or gene expression (Aim 3) of disease genes. We have assembled a team of Pediatric clinicians who are experts in GSDs, VLCAD, and MADD, as well as researchers who are experts in genetics, genomics, epigenetic regulation, biomedical engineering, and statistics. This team has obtained patient samples and received Duke IRB approval to begin immediately. We expect this study will identify and validate novel genetic variants that influence disease. While we propose to study a relatively small subset of rare disorders, these strategies will be immediately generalizable to any patient sample with any recessive disorder that has inconclusive genetic testing results. That outcome will provide comprehensive genetic testing, better understanding of disease mechanisms, and ultimately better treatment options.